(applicable when method = "quality").
object of class XStringQuality representing the quality scores
for x that are used in a quality-based method for generating a
substitution matrix.

substitutionMatrix

fuzzyMatrix

(applicable when method = "quality").
fuzzy match matrix for quality-based alignments. It takes values between 0
and 1; where 0 is an unambiguous mismatch, 1 is an unambiguous match, and
values in between represent a fraction of "matchiness".

gapOpening

(applicable when method = "quality" or
method = "substitutionMatrix").
penalty for opening a gap in the alignment.

gapExtension

(applicable when method = "quality" or
method = "substitutionMatrix").
penalty for extending a gap in the alignment

...

optional arguments to generic function to support additional
methods.

Details

When method = "hamming", uses the underlying neditStartingAt code
to calculate the distances, where the Hamming distance is defined as the number
of substitutions between two strings of equal length. Otherwise, uses the
underlying pairwiseAlignment code to compute the distance/alignment
score matrix.